[Jalview-discuss] renumbering protein sequences - working with domains not whole chains

[Ffenics]

Hi there .. I'm currently investigating how to use Jalview and DAS to annotate functional residues in protein domains. I give Jalview my own multiple protein sequence alignments.

A given protein sequence in the alignmment may, or may not,  include the whole of a protein chain. Because I won't always be using a whole protein chain,  is there a way of mapping the residue numbering as contained in the pdbs of these protein domains with the multiple sequence alignment in Jalview?

Might I be able to achieve this by mapping each sequence to its associated protein domain  (which I can provide as a pdb file) or is there another way to do this (if its possible at all).

Any help much appreciated.
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